Job ID = 6456343 SRX = SRX3380790 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:41:53 prefetch.2.10.7: 1) Downloading 'SRR6278153'... 2020-06-21T10:41:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:43:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:43:00 prefetch.2.10.7: 'SRR6278153' is valid 2020-06-21T10:43:00 prefetch.2.10.7: 1) 'SRR6278153' was downloaded successfully 2020-06-21T10:43:00 prefetch.2.10.7: 'SRR6278153' has 0 unresolved dependencies Read 8883488 spots for SRR6278153/SRR6278153.sra Written 8883488 spots for SRR6278153/SRR6278153.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:17 8883488 reads; of these: 8883488 (100.00%) were unpaired; of these: 1354656 (15.25%) aligned 0 times 4053570 (45.63%) aligned exactly 1 time 3475262 (39.12%) aligned >1 times 84.75% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2114208 / 7528832 = 0.2808 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:48:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:48:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:51: 1000000 INFO @ Sun, 21 Jun 2020 19:48:57: 2000000 INFO @ Sun, 21 Jun 2020 19:49:02: 3000000 INFO @ Sun, 21 Jun 2020 19:49:08: 4000000 INFO @ Sun, 21 Jun 2020 19:49:14: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:49:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:49:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:49:16: #1 total tags in treatment: 5414624 INFO @ Sun, 21 Jun 2020 19:49:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:49:16: #1 tags after filtering in treatment: 5414614 INFO @ Sun, 21 Jun 2020 19:49:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:17: #2 number of paired peaks: 1178 INFO @ Sun, 21 Jun 2020 19:49:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:17: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 19:49:17: #2 alternative fragment length(s) may be 49 bps INFO @ Sun, 21 Jun 2020 19:49:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.05_model.r WARNING @ Sun, 21 Jun 2020 19:49:17: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:49:17: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sun, 21 Jun 2020 19:49:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:49:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:23: 1000000 INFO @ Sun, 21 Jun 2020 19:49:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:49:29: 2000000 INFO @ Sun, 21 Jun 2020 19:49:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:49:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:49:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.05_summits.bed INFO @ Sun, 21 Jun 2020 19:49:35: Done! pass1 - making usageList (588 chroms): 1 millis pass2 - checking and writing primary data (2250 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:49:36: 3000000 INFO @ Sun, 21 Jun 2020 19:49:42: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:49:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:50: 5000000 INFO @ Sun, 21 Jun 2020 19:49:53: 1000000 INFO @ Sun, 21 Jun 2020 19:49:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:49:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:49:53: #1 total tags in treatment: 5414624 INFO @ Sun, 21 Jun 2020 19:49:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:49:53: #1 tags after filtering in treatment: 5414614 INFO @ Sun, 21 Jun 2020 19:49:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:54: #2 number of paired peaks: 1178 INFO @ Sun, 21 Jun 2020 19:49:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:54: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 19:49:54: #2 alternative fragment length(s) may be 49 bps INFO @ Sun, 21 Jun 2020 19:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.10_model.r WARNING @ Sun, 21 Jun 2020 19:49:54: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:49:54: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sun, 21 Jun 2020 19:49:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:49:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:59: 2000000 INFO @ Sun, 21 Jun 2020 19:50:05: 3000000 INFO @ Sun, 21 Jun 2020 19:50:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:10: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.10_summits.bed INFO @ Sun, 21 Jun 2020 19:50:12: Done! pass1 - making usageList (495 chroms): 1 millis pass2 - checking and writing primary data (1675 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:50:16: 5000000 INFO @ Sun, 21 Jun 2020 19:50:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:50:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:50:19: #1 total tags in treatment: 5414624 INFO @ Sun, 21 Jun 2020 19:50:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:50:19: #1 tags after filtering in treatment: 5414614 INFO @ Sun, 21 Jun 2020 19:50:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:20: #2 number of paired peaks: 1178 INFO @ Sun, 21 Jun 2020 19:50:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:20: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 19:50:20: #2 alternative fragment length(s) may be 49 bps INFO @ Sun, 21 Jun 2020 19:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.20_model.r WARNING @ Sun, 21 Jun 2020 19:50:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:50:20: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sun, 21 Jun 2020 19:50:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:50:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:50:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380790/SRX3380790.20_summits.bed INFO @ Sun, 21 Jun 2020 19:50:37: Done! pass1 - making usageList (348 chroms): 1 millis pass2 - checking and writing primary data (732 records, 4 fields): 10 millis CompletedMACS2peakCalling